chr6-54769237-G-T

Variant names:

• chr6-54769237-G-T
• rs1566753
• ENST00000763589.1:n.132+32500C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000763589.1(ENSG00000299445):​n.132+32500C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,074 control chromosomes in the GnomAD database, including 36,657 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (36657 hom., cov: 32)
• Consequence: ENSG00000299445 ENST00000763589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 4 publications found

Genes affected

ENSG00000299445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986606	XR_001744176.3	n.95+32500C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299445	ENST00000763589.1	n.132+32500C>A		intron_variant	Intron 1 of 6
ENSG00000299445	ENST00000763590.1	n.87+32500C>A		intron_variant	Intron 1 of 5
ENSG00000299445	ENST00000763591.1	n.69+32500C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103618 AN: 151956 Hom.: 36617 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.655

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.682 AC: 103703 AN: 152074 Hom.: 36657 Cov.: 32 AF XY: 0.674 AC XY: 50114 AN XY: 74328

African (AFR) AF: 0.850 AC: 35287 AN: 41514

American (AMR) AF: 0.499 AC: 7616 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5164

South Asian (SAS) AF: 0.655 AC: 3160 AN: 4828

European-Finnish (FIN) AF: 0.598 AC: 6312 AN: 10552

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44971 AN: 67972

Other (OTH) AF: 0.655 AC: 1385 AN: 2116

Alfa AF: 0.672 Hom.: 17722

Bravo AF: 0.676

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.71
PhyloP100		-0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1566753; hg19: chr6-54634035;